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(-) Description

Title :  CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH SUCCINATE
 
Authors :  R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, F. Von Delf C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Date :  04 Mar 16  (Deposition) - 16 Mar 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Tca Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Crystal Structure Of Jmjc Domain Of Human Histone Demethylase Uty In Complex With Succinate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE DEMETHYLASE UTY
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: JMJC DOMAIN, RESIDUES 878-1347
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME, U BIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2MN2Ligand/IonMANGANESE (II) ION
3SIN2Ligand/IonSUCCINIC ACID
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MN-1Ligand/IonMANGANESE (II) ION
3SIN1Ligand/IonSUCCINIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2MN-1Ligand/IonMANGANESE (II) ION
3SIN1Ligand/IonSUCCINIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1199 , CYS A:1202 , CYS A:1226 , CYS A:1229BINDING SITE FOR RESIDUE ZN A4002
02AC2SOFTWARECYS B:1199 , CYS B:1202 , CYS B:1226 , CYS B:1229BINDING SITE FOR RESIDUE ZN B4002
03AC3SOFTWAREHIS B:1014 , GLU B:1016 , HIS B:1094 , SIN B:2274 , HOH B:3154 , HOH B:3162BINDING SITE FOR RESIDUE MN B2273
04AC4SOFTWAREHIS A:1014 , GLU A:1016 , HIS A:1094 , SIN A:2267 , HOH A:3154 , HOH A:3163BINDING SITE FOR RESIDUE MN A2266
05AC5SOFTWARELYS B:1005 , THR B:1011 , HIS B:1014 , ASN B:1024 , HIS B:1094 , ASN B:1104 , MN B:2273 , HOH B:3148 , HOH B:3162BINDING SITE FOR RESIDUE SIN B2274
06AC6SOFTWARELYS A:1005 , THR A:1011 , HIS A:1014 , ASN A:1024 , TRP A:1034 , HIS A:1094 , ASN A:1104 , MN A:2266 , HOH A:3148 , HOH A:3154 , HOH A:3163BINDING SITE FOR RESIDUE SIN A2267
07AC7SOFTWAREILE B:888 , TRP B:889 , ARG B:890 , HOH B:3077 , HOH B:3350BINDING SITE FOR RESIDUE EDO B2275
08AC8SOFTWARESER A:853 , THR A:854 , GLN A:907 , PRO A:1029 , EDO A:2269 , EDO A:2273 , HOH A:3043BINDING SITE FOR RESIDUE EDO A2268
09AC9SOFTWAREEDO A:2268 , HOH A:3085 , HOH A:3387BINDING SITE FOR RESIDUE EDO A2269
10BC1SOFTWAREARG A:1077 , HOH A:3003 , ASN B:919 , GLU B:920BINDING SITE FOR RESIDUE EDO A2270
11BC2SOFTWAREHIS A:1188 , HIS A:1197 , TYR A:1222 , VAL A:1224BINDING SITE FOR RESIDUE EDO A2271
12BC3SOFTWAREGLY A:840 , ALA A:842 , GLY A:843 , PRO A:1082 , GLY A:1083 , ASP A:1084 , HOH A:3388BINDING SITE FOR RESIDUE EDO A2272
13BC4SOFTWARELYS A:816 , VAL B:1044 , ASP B:1047 , PHE B:1048BINDING SITE FOR RESIDUE EDO B2276
14BC5SOFTWAREGLN B:907 , PHE B:911 , TRP B:1101 , EDO B:2278 , HOH B:3092 , HOH B:3352 , HOH B:3353BINDING SITE FOR RESIDUE EDO B2277
15BC6SOFTWARETHR B:854 , GLN B:907 , PRO B:1029 , EDO B:2277 , HOH B:3035BINDING SITE FOR RESIDUE EDO B2278
16BC7SOFTWARELEU A:849 , GLY A:850 , SER A:853 , GLY A:1028 , EDO A:2268BINDING SITE FOR RESIDUE EDO A2273
17BC8SOFTWARELEU B:971 , THR B:972 , ARG B:979 , VAL B:980 , VAL B:981 , HOH B:3137BINDING SITE FOR RESIDUE EDO B2279
18BC9SOFTWAREGLY A:996 , TYR A:1003 , GLU A:1016 , ALA A:1106 , TRP A:1107 , ASN A:1108 , HOH A:3145 , HOH A:3154BINDING SITE FOR RESIDUE EDO A2274
19CC1SOFTWAREHIS B:864 , ASP B:957 , ASP B:960 , LYS B:963 , HOH B:3110BINDING SITE FOR RESIDUE EDO B2280
20CC2SOFTWARELYS B:1128 , SER B:1131 , CYS B:1202 , VAL B:1204 , HOH B:3236 , HOH B:3355BINDING SITE FOR RESIDUE EDO B2281
21CC3SOFTWAREGLY B:996 , GLN B:1001 , TYR B:1003 , GLU B:1016 , SER B:1022 , TRP B:1107 , ASN B:1108 , HOH B:3147 , HOH B:3154 , HOH B:3356BINDING SITE FOR RESIDUE EDO B2282
22CC4SOFTWAREARG A:1081 , SER B:914 , GLU B:918 , TRP B:1101BINDING SITE FOR RESIDUE EDO B2283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FY7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:945 -Pro A:946
2Gly A:1028 -Pro A:1029
3Gly B:1028 -Pro B:1029

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FY7)

(-) Exons   (0, 0)

(no "Exon" information available for 5FY7)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhh..........eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........eeee.....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fy7 A  801 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRRRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLS 1265
                                   810       820       830       840       850       860       870       880       890       900       910       920 ||    949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      
                                                                                                                                                   922|                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                    942                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhh.hhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhh............hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhheee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhh...........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fy7 B  802 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSSSSAENL 1272
                                   811       821       831       841       851       861       871       881       891       901       911       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      
                                                                                                                                                920|                                                                                                                                                                                                                                                                                                                                      
                                                                                                                                                 946
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5FY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FY7)

(-) Gene Ontology  (10, 10)

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  5fy7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UTY_HUMAN | O14607: 3zli 3zpo 4uf0 5a1l 5fxv 5fxw 5fxx 5fxz 5fy0 5fy1 5fym

(-) Related Entries Specified in the PDB File

5fxv CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N05859B
5fxw CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH FUMARATE
5fxx CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH OXALOACETATE
5fxz CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH CITRATE
5fy0 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH L-MALATE
5fy1 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N08619B
5fy4 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH SUCCINATE
5fy5 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH FUMARATE
5fy8 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO-ISOCITRATE
5fy9 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH PYRUVATE
5fyb CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
5fyc CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE
5fyh CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE
5fyi CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE
5fym CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fys CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fyt CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N09996A
5fyu CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10042A
5fyv CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH OXALOACETATE
5fyy CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N05798A
5fyz CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10063A
5fz0 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N11213A
5fz1 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH E48115B
5fz3 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N08776B
5fz4 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10057A
5fz6 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT N05859B ( LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fz7 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT ETHYL 2- AMINO-4-THIOPHEN-2-YLTHIOPHENE-3-CARBOXYLATE (N06131B ) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fz8 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MALATE